Intrigue in the Flophouse.

I believe that it has to do with the fact I already entered the commander building ( in the stolen drive core ). The game probably wants that flophouse first, stolen core second ?

Well, what I am saying is there are 2 different ways :

1. defeating the flophouse first by going through the open and shut door/gate.

2. going around and find another entrance to get the stolen drive core. So if I get the core and finish up the whole commander center ?

Important rule of thumb with RPGs - and Bioware RPGs in particular - you almost always need to complete optional objectives before completing a quest-advancing objective, or else you're going to miss out on content and rewards. Some principle with story-advancing key quests and certain side quests.

As someone who enjoys both completionist play and immersion, I dislike metagaming too much by managing the order of quests, but it's something you try to strike a balance on so you're able to go with the flow while playing but not missing out on things as well.